Hello,
this is a little bit hard to tell from the outside. So for the moment I have
only some general ideas:
Did the algorithm converge in both cases? If not, I would have less confidence
in the results.
One thing to consider besides the effect size and direction is the variability
of the est
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Hello FreeSurfer Experts,
I am trying to calculate Cohen's d effect sizes for a contrast I created in
QDEC. I have found multiple sources suggesting this code:
cd glmdir/contrast
fscalc gamma.mgh div ../rstd.mgh -o cohensd.mgh
But when I use it (replacing the glmdir and contrast with my own), I
if they are different sizes, then something is wrong. Try deleting the
folder and re-running qdec.
On 4/17/18 9:04 AM, Kelly Vaughn wrote:
Hello FreeSurfer Experts,
I am trying to calculate Cohen's d effect sizes for a contrast I
created in QDEC. I have found multiple sources suggesting this
Dear experts,
I encountered a problem when trying to open freeview. I am using FreeSurfer
v.5.3.0-HCP, and after sourcing it, I tried typing simply freeview in the
terminal, as described in this link:
http://freesurfer.net/fswiki/FreeviewGuide/FreeviewGeneralUsage/FreeviewQuickStart
but the feedbac
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Hi Darko, how are you sourcing freesurfer? And what is the output of running
“which freeview” and “which freeview.bin”?
best,
Andrew
From: on behalf of Darko Komnenić
Reply-To: FS Help
Date: Tuesday, April 17, 2018 at 11:17 AM
To: FS Help
Subject: [Freesurfer] unable to open freeview
Dear
Hi Andrew,
FreeSurfer is being sourced automatically each time I open the terminal,
and I see the usual lines:
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /home/lisak/Desktop/freesurfer
FSFAST_HOME /home/lisak/Desktop/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
S
Hi,
I'm trying to deface an MEMPRAGE dataset using the following command:
[jazz:test_deface] (nmr-stable53-env) mri_deface outSubDir/mri/orig/001.mgz
talairach_mixed_with_skull.gca face.gca sample_T1_input_defaced.mgz
and am getting the output:
logging results to sample_T1_input_defaced.lo
Can you ls /usr/local/freesurfer/stable6/bin
If so, you could put that at the start of your path to get the release 6
binaries.
-rob
On Apr 17, 2018, at 11:39 AM, Warner, Graham Cary
mailto:gwar...@mgh.harvard.edu>> wrote:
Hi,
I'm trying to deface an MEMPRAGE dataset using the following comma
Not really. Are you trying to account for B0 distortion in the DTI? If
you have a B0 map, you can pass that to bbregsiter and mri_vol2vol to
account for it
On 4/16/18 10:29 AM, Hedyeh Javaheri wrote:
Hello all,
I am performing DTI analysis and wanted to know if Freesurfer has a
tool for non
You need to put in age, weight, AND age*weight. If you have two classes
and use DODS, then the contrast would be
0 0 0 0 0 0 0.5 0.5
On 4/13/18 8:02 PM, David S Lee wrote:
Hi Douglas,
Thank you for your reply.
To follow up, I am setting up GLM analysis with 1 categorical variable
and 1 co
That worked, thanks!
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Dicamillo, Robert
Sent: Tuesday, April 17, 2018 11:47:02 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_deface keeps seg faulting
Can you ls /usr/local/freesurfer/stab
Map the annotation into the indididual subject space with
mris_apply_reg. Then create a segmentation from the annotation using
mri_aparc2aseg. Look inside any recon-all.log file for an example
command line. You will need to change the annot and the output. Then run
fcseed-config specifying the
sorry for the delay, see below
On 4/14/18 10:00 AM, Boggess, Matthew Jozsef wrote:
Hello,
I just wanted to follow up to see if anyone could help with any of my
questions, particularly # 1.
Thank you!
Matt Boggess
Run it for each subject using -f subject/stats/lh.lobesStrict.stats,
then use aparcstats2table with -p lobesStrict to get a summary across
all subjects
On 4/16/18 7:18 AM, Fernanda Hansen P. de Moraes wrote:
Douglas,
I'm already extracting the data with mris_anatomical_stats -a
SUBJ225/labe
On 4/16/18 11:56 AM, Sarah Cole wrote:
Hi Doug,
I need your recommendations on two topics. I really appreciate your help.
1.) I have two runs of the same experiment, each for about 12 minutes.
These 2 runs are different only in the presentation order of the
stimuli. I also have one localize
sorry for the delay ...
You will definitely need to change the contrast values so that the
positives and negatives both add to the same number (with opposite
sign). It is a bit of a judgement call in terms of removing them
entirely. With an unbalanced design, you cannot remove the fixed effect
Do you have tcsh properly installed? You can check by running the command “tcsh
--version”.
If it is installed, I’m not quite sure why you’re experiencing this problem,
but I would suggest modifying the freeview script at
/home/lisak/Desktop/freesurfer/bin/freeview to debug. Try adding the foll
Yes, that looks correct. If you are interested in the offset, you should
probably demean the thickness. You can do this by running
mri_glmfit --y rh.thickness.10B.mgh --osgm --surface fsaverage rh --o
glm.thickness --save-eres
This will produce a file called eres.mgh in the output. This is th
There is not an easy way to do this. If you have access to the original
hammersmith data, you can run each subject through FS, copy/convert the
manual labels into the conformed space for each subject, then build your
own volume-based atlas. If that is something you are up for, let me know
and I
Sorry, just seeing that you also want cortical summaries. Those might be
easier. You should run recon-all on the T1 template for the hammersmith.
You can then create your own hammersmith annotation by mapping the atlas
labels onto the surface (mri_vol2surf) and then mris_seg2annot. You can
then
Hi Andrew,
thanks for getting back so quickly.
Here are the outputs:
“tcsh --version” gives a "tcsh 6.18.01 (Astron) 2012-02-14
(x86_64-unknown-linux) options wide,nls,dl,al,kan,rh,nd,color,filec"
I added echo $PATH right before the “freeview.bin $argv” line in the
freeview script, and the output
something strange is going on because that mri_vol2vol command has
worked for years. Can you upload your subject's dir to our filedrop?
https://gate.nmr.mgh.harvard.edu/filedrop2
On 4/16/18 5:40 PM, Michelle VanTieghem wrote:
Hi Bruce,
If I *just run the mri_convert command that you provided,
You should read the FDR paper for more detail. But the FDR is the number
of false positives relative to the total number of positives. The way it
is interpreted is that when you look at an image, 5% of the voxels above
threshold are false. You don't know which 5%. If the 5% came out of a
big bl
also, not sure if this info will be useful, but
libvtkverdict.so.5.6
exists on my computer in /home/lisak/Desktop/freesurfer/lib/vtk/lib/vtk-5.6
subfolder,
but from the error message above it seems as if Freesurfer expects the file
to be located in lib/vtk/*bin *subfolder.
On Tue, Apr 17, 2018 at
Hi Darko, the freeview wrapper script sets up libraries used by freeview.bin,
so the error you get when only calling freeview.bin is expected. There is
something odd going on with your PATH after sourcing the TCL package. Can you
send me your tcl_setup file in $FREESURFER_HOME/bin?
It would als
Hi Andrew,
OK, so here is what happened:
After adding the echo $PATH under the first line, my output is now this:
"/home/lisak/miniconda3/bin:/home/lisak/Desktop/freesurfer/b
in:/home/lisak/Desktop/freesurfer/fsfast/bin:/home/lisak/
Desktop/freesurfer/tktools:/home/lisak/Desktop/fsl/bin:/
home/lis
Hi Darko, there’s a big difference between using single vs double quotes in
shell scripting – single quotes prevent variable expansion. Your modification
to tcl_setup actually renders your PATH completely unusable. The quote syntax
in the setup scripts shouldn’t cause any problems, and your unma
Hi Doug,
I am able to get up to the mrs_glmfit step of the Surface Based Group fMRI
Analysis, but it does not indicate how a comparison should be made between the
two groups that I have. It only gives information on how to perform a one
sample group mean test (osgm). In addition, when you menti
Hi Andrew,
thanks a lot for your feedback!
I renamed the original fine, so it is now called just tcl_setup, and here
is the output I got after typing "freeview"
/home/lisak/miniconda3/bin:/home/lisak/Desktop/freesurfer/bi
n:/home/lisak/Desktop/freesurfer/fsfast/bin:/home/lisak/
Desktop/freesurfer/
Are you using a bash shell? If you are, there should be a file located at
~/.bashrc (it’s a hidden file in your home folder)
Andrew
From: Darko Komnenić
Date: Tuesday, April 17, 2018 at 2:24 PM
To: "Hoopes, Andrew"
Cc: FS Help
Subject: Re: [Freesurfer] unable to open freeview
Hi Andrew,
than
Hi Doug,
Thank you for your response. I attempted to run recon-all on the Hammersmith
nifti file as suggested, but unfortunately it appears to have run into some
issues. I’ve attached the recon-all.log for reference.
Best,
Ryan
--
Ryan Flores
Clinical Research Coordinator
From: on behalf of D
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